Abstract

Population transfer between vibrational eigenstates is important for many phenomena in chemistry. In solution, this transfer is induced by fluctuations in molecular conformation as well as in the surrounding solvent. We develop a joint electrostaticdensity functional theory map that allows us to connect the mixing of and thereby the relaxation between the amide I and amide II modes of the peptide building block -methyl acetamide. This map enables us to extract a fluctuating vibrational Hamiltonian from molecular dynamics trajectories. The linear absorptionspectrum, population transfer, and two-dimensional infrared spectra are then obtained from this Hamiltonian by numerical integration of the Schrödinger equation. We show that the amide I/amide II cross peaks in two-dimensional infrared spectra in principle allow one to follow the vibrational population transfer between these two modes. Our simulations of -methyl acetamide in heavy water predict an efficient relaxation between the two modes with a time scale of 790 fs. This accounts for most of the relaxation of the amide I band in peptides, which has been observed to take place on a time scale of 450 fs in -methyl acetamide. We therefore conclude that in polypeptides, energy transfer to the amide II mode offers the main relaxation channel for the amide I vibration.

Received 02 April 2008Accepted 27 June 2008Published online 05 August 2008

Acknowledgments:

T.l.C.J. acknowledges the Netherlands Organization for Scientific Research (NWO) for support through a VENI grant. Andrei Tokmakoff and Lauren DeFlores are gratefully acknowledged for providing their experimental data. The authors thank Ria Broer for helpful discussions.